Dr Ibrahim Abu Mohamed and several other Australian Muslim clerics met with Indonesian Religious Affairs Minister Lukman Hakim Saifuddin to plead for mercy.

"On behalf of the Islamic community of Australia, we plead, with respect and humility, for mercy for the lives of two young Australian men, who have not only shown repentance for their serious crimes, but have rehabilitated themselves and indeed others," Dr Abu Mohamed said in a statement.

Dr Abu Mohamed said the delegation of Islamic leaders respected the position of the Indonesian government in its firm pursuit of the drug scourge.

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"We offer no criticism of the justice system in recent cases," he said.

"However, we note that mercy and forgiveness lies at the heart of Islam for those who repent and have reformed their ways. We urge that the heritage of mercy in our religion is fully and deeply considered in the application of state law."

Dr Abu Mohamed is a well known Muslim scholar who was appointed Grand Mufti by the Australian National Imams Council in 2011.

He taught Islamic studies in Abu Dhabi and then founded radio station Quaran Kareem Radio, which broadcasts religious programs, when he moved to Sydney in 1997.

The Grand Mufti was accompanied by Sheikh Mohamed Khamis, the Vice President of the NSW Islamic Council and imam for the Newcastle mosque, Sheikh Dr Amin Hady, chairman of the foundation of Islamic studies in Australia and imam of the Zetland mosque in Sydney and Sheikh Kafrawi Hamzah, an Islamic scholar and imam of the Parafield Gardens mosque in Adelaide.

Sheikhs Hady and Hamzah are of Indonesian background.

This is the spirit of Islam.

Dr Ibrahim Abu Mohamed

The delegation did not take questions due to the "very sensitive nature of this matter".

They also emphasised they attended the meeting on behalf of the Islamic community of Australia and the initiative was independent of the Australian government.

Dr Abu Mohamed said the delegation intended to meet with other Indonesian Islamic leaders to put the case for mercy and forgiveness.

"This is the spirit of Islam," he said.

Mr Lukman said he would report the discussion to the Indonesian cabinet.

He said the Government and religion could not intervene in the legal system.

"However I can convey what the Australian government and the Australian people feel about this case," he said.